It's pretty hard to say who would win between Yamato and Queen because they're both 2 very different types of fighters. However, after taking a look at their individual skills, standard tactics, and how they'd interact with each other, I think these are the main factors that will decide the fight:
Versatility: Queen. He has access to a wide variety of abilities. Spammable exploding lasers, voice activated rocket launchers, virus-containing cannon balls and bullets, various limbs that can be used to attack from all angles, Poison Pink's abilities to attack directly with poison without relying on plague rounds, electricity and flames to coat his attacks with, antibodies for his plagues, extendable body parts for more rage, 2 swords for added lethality, invisibility, and durability negating crushing attacks. Yamato does have some ranged abilities and can freeze objects with her frost breath or by coating attacks in ice.
Haki: Yamato. She has stronger Buso and also has advanced Haō. Queen's Buso isn't terrible per se but he just lacks the feats to say that it's on Yamato's level. Yamato has some pretty unremarkable Kenbun though considering she needed to rely on Momonosuke to tell what was going on on the rooftop, while other Haki users such as Kaidou, Law, Kid, Sanji, Marco, etc could use their Kenbun to sense all over Onigashima. However, she has been shown to be able to sense power levels.
Endurance/Stamina: Queen. Yamato can (very arguably) take stronger attacks than Queen can thanks to her durability, but Queen can definitely withstand more damage. Chopper attacked Queen for 20 minutes straight and made him question if his attacks were even properly landing. Marco landed several attacks on Queen but failed to deal lasting damage. Sanji specifically couldn't break through Queen's toughness and make him feel real pain even when using durability negating attacks. Queen scales above Jack in endurance who after 5 continuous days of fighting showed no sign of fatigue. He also scales above Ulti who could take a point-blank Thunder Bagua from Yamato and then go on top chase her right after, fight Usopp + Nami, and then take Big Mom's Maser Cannon.
I honestly think Queen takes this. The mixture of Queen's endurance (which is good enough to take many attacks from Yamato) and Yamato's lack of any durability negating attacks makes it hard to believe that she'd be able to take Queen out in a reasonable timeframe before Queen overwhelms her with his hax and range as well as the weight and unrelenting nature of his fighting style.
Hybrid Yamato and Hybrid Queen should have relative combat and reaction speeds since they have similar scaling. Their amps should also be similar in speed since they're both layered blitzes. Thunder Bagua's speed amp allowed Kaidou to blitz Law, who could blitz Mother Misery. Henry Blazer's speed amp is superior to the amp Niji used to blitz Sanji, who blitzed him earlier.
Yamato's Haki would be really helpful here since it could help her avoid getting taken out quickly by Queen's fire, electricity, and poison, but because of Queen Flying Pan style of fighting in which he uses all of his limbs and weapons to attack all at once, I don't think Yamato would be able to constantly use Haki to defend herself. Full-body Buso coating takes too much stamina and her Kenbun has too many anti feats to say that she'd be able to consistently turn on Buso at the spots where Queen's attacks hit
like Katakuri and Luffy. Yamato's ice armor could
technically be used to substitute Haki defense, but at the end of the day it's just an armor. Haki gives actual resistance to Queen's abilities while the ice armor only acts as a momentary defense tool that can be easily broken. Other than defending attacks, Yamato's Haki can also be used to increase the effectiveness of her ice attacks, as Haki grants resistance negation (
although this can be countered by Queen's Ice Oni virus antibodies).
Queen has much larger combat range than Yamato, as every single one of his attacks can come from a several tens of meters away. Because Yamato fights with her Kanabo at a close range, this would make it difficult for her to land any hits, which becomes even worse with Queen's invisibility.